This is not strictly speaking a bug since it does not impact anything,
but I would like to assume that identifiers can't be bound multiple times
(in my backend patches) and this is the only case I know (in the opam
repository) where this don't hold.

Multiple binding of the same identifier is a bug: there are already parts of the backend where this invariant is assumed, and I have generated wrong code by just breaking it.
Whether to merge the branches or not is another question.